Family members of those killed in the 9/11 attacks have expressed anger over displays of defiance shown by the alleged plotters during an arraignment hearing at Guantánamo Bay.

The hearing, which was expected to last two hours, stretched to 13 hours as Khalid Sheikh Mohammed and his four co-defendants refused to accept the start of trial proceedings in a controversial “military commission” inside the US naval base in Cuba.

The hearing was marked by near-farcical scenes in which the defendants prayed, read the Economist, talked among each other and ignored the judicial events around them.

Eddie Bracken travelled from Staten Island in New York to Guantánamo, having won, by lottery, one of six places set aside for 9/11 family members at the arraignment hearing. His sister Lucy Fishman died in the Twin Towers in New York.

“I felt very angry,” he said, referring to the silence maintained by the five accused through most of Saturday. “They are complaining [about the trial] but our families can’t complain no more. They took my sister’s life. I wouldn’t care if they were on a bed of nails, but it’s our justice system and they have rights.”

Bracken said that he had been particularly aggrieved when some of the defendants ignored the court proceedings and began talking among each other. “That wasn’t right. My sister who was lost can’t converse with anybody.

“When they get put to death or locked down for the rest of their lives they shouldn’t be allowed to converse with anybody ever – solitary life forever.”

Family members watched Mohammed, who has not been seen in public for about three years, from behind a thick glass wall. The alleged architect of 9/11 sat silently through most of the hearing stroking his henna-dyed beard, wearing a white turban and tunic. Walid bin Attash, a Yemeni accused of having researched flight simulators for the 9/11 hijackers, refused even to attend the hearing and was brought into it against his will strapped into a restraint chair.

“They’re engaging in jihad in a courtroom,” said Debra Burlingame, who watched the arraignment as it was shown by live feed in a special facility in Brooklyn. Burlingame’s brother, Charles, was pilot of the plane flown into the Pentagon.

Family members said that listening to the details of 9/11 reinvoked by the hearing brought back painful memories. “It brought back all the memories of that day,” Bracken said.

The arraignment underlined what observers of the 9/11 prosecutions have long suspected – that this is going to be a very drawn out and contentious affair. The military judge at the proceedings – Army Colonel James Pohl – indicated that it would be at least a year before the trial began.

Once it does get going, it might then drag on for several years. Army Brig Gen Mark Martins told reporters on Sunday that with the defence having filed hundreds of motions challenging the specifics of the military commissions there would be no speedy end.

“I am getting ready for hundreds of motions because we want them to shoot everything they can shoot at us,” he said.

The idea of subjecting the alleged mastermind of 9/11, Mohammed, to military justice has been hotly disputed from the start. The Obama administration had preferred to try him under civilian law, but backed off when the idea of holding a trial in New York close to Ground Zero generated massive local opposition.

Martins tried to justify the military trial system, insisting it would extend to the five defendants their full legal rights. “We are giving them every fairness as a matter of statute and a matter of fairness.”

He added that the process would balance a fair trial with the need for public access to the proceedings and defence of national security. “I believe transparency is absolutely critical in this issue because we have a lot of contentious issues and I want as many people as possible to understand them,” Martins said.

One of the most contentious of those issues is torture. Defence lawyers at the arraignment attempted to raise the question but were slapped down by Pohl who said: “We’ll get to it when I said we’ll get to it”.

It is known that Mohammed alone was subjected to simulated drowning, or waterboarding, 183 times.

Speaking after the arraignment, defence lawyer James Connell said the behaviour of the five defendants had amounted to “peaceful resistance to an unjust system”. He said the scenes in the courtroom had demonstrated “that this will be a long hard-fought but peaceful struggle against secrecy, torture and the misguided institution of the military commissions”.